Woden General Duties Acting Sergeant Colin Giumelli, who has experience with the Criminal Investigations fraud squad and as an investigator on Christmas Island, was called after $42,000 was discovered to be missing by the business in early May last year.

Acting Sergeant Giumelli told Fairfax Media his experience in fraud cases made him suspect the alleged fraud was larger than it appeared.

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"Through a couple of other jobs I'd done in the past, I told the complainant I didn't feel that this would be the only matter, I asked them to go back and conduct further audits into their account," Acting Sergeant Giumelli said.

"They've come back to me a couple of weeks later and I think at that point it was up to $130,000, and then I started the ball rolling with the banks," he said.

The officer, assisted by the Woden General Duties team and the fraud squad, spent hundreds of hours investigating the allegations.

He worked with the Phillip-based company and a number of major banks to gradually uncover a much larger string of fraudulent payments.

The employee is accused of conducting 105 fraudulent transactions totalling about $987,000, between November 2008 and February 2012.

He allegedly abused a position of trust to make fraudulent payments, paying falsified bills with company funds to funnel into "known accounts".

The employee was on a form of leave when the missing funds were first discovered, Acting Sergeant Giumelli said.

"It's larger and more complex than any investigation that I did with the fraud team," Acting Sergeant Giumelli said. "The experience that I had with the fraud team led me to feel comfortable continuing the investigation," he said.

A series of civil proceedings are currently underway in an attempt to recover the missing funds.

The police investigation culminated in eight search warrants, on the man's Forde home and on a series of bank accounts.

The man is now expected to appear in the ACT Magistrates Court on January 25, with police planning to summons him at a later date.